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DatoValore
TitleEffects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data
Abstract Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The generalised mixed Yule coalescent (GMYC) and the Poisson tree process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes. Here, we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2000 separate species delimitation analyses across 16 empirical data sets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses. 10.1111/(ISSN)2041-210X
SourceMethods in ecology and evolution (Online) 5 (10), pp. 1086–1094
KeywordscoalescentDNA barcodingGMYCmetabarcodingmolecular datingNGSOTUPTPspeciationspecies delimitation
JournalMethods in ecology and evolution (Online)
EditorWiley, [Bognor Regis], Regno Unito
Year2014
TypeArticolo in rivista
DOI10.1111/2041-210X.12246
AuthorsCuong Q. Tang; Aelys M. Humphreys; Diego Fontaneto; Timothy G. Barraclough
Text293810 2014 10.1111/2041 210X.12246 ISI Web of Science WOS 000344598300012 coalescent DNA barcoding GMYC metabarcoding molecular dating NGS OTU PTP speciation species delimitation Effects of phylogenetic reconstruction method on the robustness of species delimitation using single locus data Cuong Q. Tang; Aelys M. Humphreys; Diego Fontaneto; Timothy G. Barraclough Imperial College London; Stockholm University; Consiglio Nazionale delle Ricerche CNR Coalescent based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The generalised mixed Yule coalescent GMYC and the Poisson tree process PTP are methods that use ultrametric GMYC or PTP or non ultrametric PTP gene trees as input, intended for use mostly with single locus data such as DNA barcodes. Here, we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2000 separate species delimitation analyses across 16 empirical data sets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes real anomalies or methodological artefacts affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model based gene tree e.g. RAxML and GMYC approaches with BEAST trees for obtaining species hypotheses. 10.1111/ ISSN 2041 210X